Office 365 – Merging 2 Mailboxes To Single User CLI

First, You need to give yourself membership the Discovery Management role and add the Mailbox Import Export role to the Discovery Management role.
The content will be placed in a top level folder not merged with the main folder tree, but once in there the content can be dragged out to the main tree as required.
 
Run Powershell as admin:

Search-Mailbox -Identity "MAILBOX1" -TargetMailbox "MAILBOX2" -TargetFolder "Moved From Old Mailbox" -LogLevel Full

 

*Once done you can run the above against any mailboxes.
**Alternatively, you can use a search process to copy the entire content from one mailbox to a folder in a target mailbox.